How to bake alpha in Cycles?
I don't think it's possible to bake alpha directly, but you can try making a new shader mixing a white and a black emit shader together using the alpha of your textures as mask, then bake that into a new texture.

It will be a bit tedious if your scene is too complex, but I don't know of any other way. If you have too many objects it's probably a good idea to try to automate that using python.